


Like Ships in the Night

by oywiththepoodles



Category: Agents of S.H.I.E.L.D. (TV)
Genre: Alternate Universe - Canon Divergence, Gen
Language: English
Status: Completed
Published: 2014-10-17
Updated: 2015-03-17
Packaged: 2018-02-21 12:43:59
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 6
Words: 3,754
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2468618
Author URL: https://archiveofourown.org/users/oywiththepoodles/pseuds/oywiththepoodles
Summary: <blockquote class="userstuff">
              <p>Fitz gets back in the field and Jemma does her best to avoid him. Mostly.</p>
<p>spoilers up to 2X03</p>
            </blockquote>





	1. Coffee

Coulson was not an anxious man by any standards. But with Simmons a half hour late for an emergency meeting she had broken protocol to call for, he was starting to worry. Simmons was almost never late. Terrible images of what could have held her up floated through his head. When she finally slid across from him in the back booth, a wave of relief washed over him.

That was until he got a good look at her. She had always been pale, but today she was down right translucent and the dark circles under her eyes stood out in stark contrast. 

“You look like shit- when was the last time you slept?”

“No rest for the wicked and such...” she trailed off, signaling to the waitress for coffee.

“So what’s the emergency?”

“How is Fitz?” she asked

Coulson couldn’t help but be annoyed. “He’s fine. But I’m sure you didn’t call from a pay phone and drag me here at the crack of dawn to ask about Fitz.”

“Is he really fine though?” she persisted. “Is he...capable?”

“What’s going on Jemma?”

Jemma slipped a manila folder onto the table between them, opening it to reveal a standard report on a comparatively boring 084. The picture showed what looked like 4 glass rods, roughly 6 inches each. Of course they weren’t glass. A cursory glance at the file told Coulson the rods were of an unknown material from an unknown place and served as a power source- alien battery technology. As the waitress approached, she closed the file and shoved it firmly in his direction. 

“This is Fitz’s Moby-Dick,” she said simply. 

Simmons accepted the cup with a murmur of thanks and reached for the milk and sugar. Coulson raised his eyebrows at her change from tea to coffee but said nothing. Simmons gave a sheepish shrug in response and took a sip. When the waitress was out of earshot, she leaned in towards Coulson and began to whisper.

“Back at the academy, Fitz used to entertain himself by reverse engineering any alien tech he had access to. There weren’t a lot available to us, especially not early on. But this particular one was considered so benign, and we were so advanced, that our professor gave us the rods themselves.”

“It wasn’t long before Fitz realized these rods were wildly misunderstood. He was convinced that they weren’t just energy sources, but keys to something more powerful, something really dangerous. He tried for months to convince our professor of the rods’ importance but to no avail. And because of the unorthodox way we came by the rods, we couldn’t exactly report it to anyone either. It drove Fitz _crazy_ to keep this ourselves.”

A ghost of a smile settled on her face as she sat lost in thought, undoubtedly remembering a young and crazy Fitz. For a moment, Coulson could see the remnants of the bright eyed girl she used to be. Then she frowned.

“Of course, that professor turned out to be Hydra, so it makes sense that he didn’t share Fitz’s discovery the with proper SHIELD authorities. And it probably explains why he let us work with the rods themselves in the first place.”

“So where are the rods now?”

Jemma sighed. “Hydra has them- and they know they are part of something powerful. My superior has been looking for the missing piece. Of course, if he had half the brain that Fitz has, he’d realize that he’s already found it.” 

Here she stopped to pull out a second manila folder and slide it to Coulson. “When Fitz gave up arguing with our Professor, he took to speculating on what he called the ‘weapon of mysterious destruction.’ He drew thousands of sketches, but one was his favorite.”

Coulson opened the folder.

“This has to be it. Its similarity to Fitz’s sketches can’t be a coincidence. This is what Fitz has been dreaming of since he first laid eyes on the rods.”

“And Hydra hasn’t made the connection yet?”

“Fortunately, no. They have a long list of potential candidates, and from what I can tell this one is practically at the bottom. That buys us some time, but not a lot. It’s only a matter of time before they figure out that I know something about the rods and pull me in for questioning.”

“So you need to know if Fitz is ready to go into the field, to destroy the weapon before Hydra figures it out?”

Jemma nods. “It’s that, or I blow my cover and destroy the rods. We can’t let this weapon fall into their hands.”

“Keep your cover, no matter what. We will handle this.”

Jemma let out a breath she had been unconsciously holding and wrapped her hands around her mug.

Coulson looked down at the file in his hands. “What does it do?”

Jemma bit her lip. “I don’t know exactly- but to hear Fitz tell it, we don’t want to find out.”


	2. Are you crazy?

Coulson stood in front of his team with some trepidation. Despite what he told Jemma, he wasn’t sure Fitz was ready. 

True, Fitz had been thriving in the lab lately. With the help of Mack or even Hunter, he could take on almost everything that came his way. Still, he wasn’t as fast as he once was and there were, of course, those odd moments when he stared off into space, muttering to himself.

On the other hand, having Jemma in Hydra had been crucial. He just couldn’t afford to lose the valuable information she provided. Mind made up, he took a deep breath and began.

“Hydra is looking for a weapon of immense power. I don’t know what this weapon does, but I know they are days away from finding it- a week at most. And thanks to our source, we’ve got the jump on them. We know what it is and where it is. We need to act immediately.”

He turned to Fitz. “We’re going to need you in the field for this one.”

Trip raised his eyebrows. 

“Sir,” Skye interjected “Couldn’t we just bring the weapon back to base and let Fitz work on it here?”

“Not an option.” Coulson said decisively, his gaze fixed on Fitz. “What do you say? Are you ready to get back in action?”

Fitz looked down, suddenly finding his shirt buttons very interesting. “Sir, you’ve got more than a few qualified engineers. Surely they’re..ehm...ehm..safe, the safer option.”

“None of them have your experience with alien tech. Plus, I have it on good authority that you are the right man for this job.” 

The team silently waited for Fitz to say something. He wrapped his arms around himself and squeezed his shoulder, as if for reassurance. Finally, he nodded. “What sort of weapon are we talking about?”

Coulson pulled up a picture of the weapon. 

“You’re kidding,” Skye scoffed. “ _That’s_ a weapon? A pyramid?”

“The Great Pyramid of Giza, to be exact. And technically it’s more like part of a weapon.” Coulson gave Fitz a sidelong glance before pulling up a picture of 4 glass rods. “This is the other part.”

Like a fish, Fitz opened and shut his mouth as he struggled to find the right words- or any words for that matter. When none came to him, he finally settled for a terrifying scream of rage. With incredible speed that shocked the team, he jumped over the table and lunged at Coulson. Fortunately, Mack managed to intercept Fitz before his outstretched hands could reach Coulson’s neck.

“JEMMA? JEMMA!?!”

“Yes” was all Coulson said, letting Fitz work through it. 

“JEMMA IS YOUR SOURCE?ARE YOU CRAZY?” Fitz struggled wildly against Mack’s hold in attempt to reach Coulson. “ **JEMMA??!!!** ”

“Yes.”

Fitz turned his head suddenly to yell at the empty space just between Skye and Coulson. “GET YOURSELF KILLED!...UNBELIEVABLE... YOU’RE...SHE’S...TERRIBLE LIAR!”

“Actually, she’s gotten much better at it,” Skye cut in.

“You KNEW?” This realization seemed to knock the wind out of Fitz. He slumped against Mack, looking at his team members in turn. “You all knew? How long?”

“She’s been Hydra since she left,” May said.

“I didn’t know until the Donnie Gill mission,” Skye commiserated. “And I took it about the same as you, though with slightly less arm flailing.” She reached out to rub Fitz’s arm sympathetically.

Once again, words failed Fitz.

Coulson seized the opportunity. “I’m confident in Simmons’ abilities, and I’m confident in yours, Fitz. You and I can discuss this later but right now, we have a mission to do. May, chart a course, we need to be at that pyramid by sundown.”


	3. Chapter 3

“Miss Simmons, come with me.”

Jemma put down her pipette and steeled herself. She knew Hydra’s research on the rods would eventually lead them to her, but she thought she had more time. It’d been less than 24 hours since she sat with Coulson in the roadside diner. 

Bakshi lead her to his office. She’d been there a handful of times since the Donnie Gill incident, but it still made her nervous. At least she wasn’t being escorted by large armed guards this time.

Seated across from his desk, she gave him her best earnest look. “How can I help you today?” she asked brightly.

He motioned to the file at the edge of his desk. She reached for it, hoping against hope that it wasn’t the rods. Coulson needed more time, and she didn’t know how long she could keep the weapon from Hydra without blowing her cover. To her surprise and horror though, the file contained not the rods, but the pyramid with which she was so familiar.

“You look surprised, Miss Simmons.”

She took a moment, as if she were really studying the folder. In her head she recited her mantra- half truths, half truths- and then looked up at him.

“Synchronicity always surprises me- I spent a lot of time looking at this file yesterday so it’s funny that you brought me up to discuss it today. Logically, I _know_ that causality or probability can explain the coincidence, but it is amazing how much it _feels_ like something more-intuition, even ESP...” 

Jemma had always had a tendency to go off on tangents. She had strived unsuccessfully to lose the habit back at academy, but now she was glad for it. It was an authentic and believable way for her to deflect the conversation and buy time. She nursed it for all it was worth.

“My favorite example of synchronicity is that of the plum pudding. Do you know that one? Émile Deschamps-”

“Miss Simmons, do control yourself.”

Jemma closed her mouth with a soft pop and blushed.

“Yes, I know you were looking at this file. The question is why?”

“Ah, so causality it is.” She swallowed. “When I finish my work early, I like browse the 'to be assigned' list- see what’s on deck, as it were. Sometimes, I entertain myself by guessing who will be assigned what. So far I’ve been quite good at this game...”

“Again, this I know. You always finish early, and you alway browse the list.”

Jemma looked down. She hadn’t realized her activities were so closely monitored.

“But you never examine a file for-” he looked down to check his notes “-for nearly 27 and a half minutes. What is different about this one?”

She was silent- half truths, half truths.

“Miss Simmons?”

“Well, it’s embarrassing really. At the risk of sounding like a school girl, I was feeling a bit sentimental. A good friend of mine had a theory that the pyramids were actually alien tech very cleverly disguised. Whenever he had slightly too much to drink, this was all he could talk about. Well, this and monkeys.”

Jemma felt her eyes well up at the memory of a very drunk Fitz enthusiastically advocating for a lab monkey. Feeling sentimental was an understatement. 

“He used to sketch it out on bar napkins.” She gave Bakshi a watery smile. “When I saw this on the list, I couldn’t help but look at it.”

“I assume you are talking about Leopold Fitz?”

Not trusting her voice, Jemma simply nodded.

“He is still with SHIELD, correct?”

She nodded again.

“Should we be concerned that he will be able to harness this tech for SHIELD?”

“No.” Jemma looked up sadly. Hoping what she said next was an outright lie, she added “That Fitz is long gone.”

“That’s a shame. He would have been a great asset to Hydra. Well, as it is on the list of tech to researched, and you seem to be familiar with it already, you will do the recon. Let’s see if any of Mr. Fitz’s theories were correct. Be ready to leave tomorrow at 0400.”


	4. Pure Genius

“Fitz, how much longer?” 

May was getting antsy. Fitz, Mack, and Skye had been down in the subterranean chamber for almost 5 hours now, and from what she could tell, Fitz hadn’t touched a thing yet. Under the cover of night, she could easily hold the only way in and out of the pyramid. But the sun would be up soon and then they’d all be in trouble. They were running out of time. 

“Fitz?”

“This is a dangerous weapon of unknown alien origin! It cannot be rushed. The thing, about this, well...I need to...it just-”

“I think what Fitz is trying to say, is back off, he’s working on it,” Mack snapped into his com.

“Yes. That.” Fitz muttered, before flopping to the ground. Skye furrowed her brow, looking at Mack for answers. He just shrugged in response.

“Well, the sun is almost up. You’ve got an hour to get back on the Bus, whether or not you’ve finished the job. We can come back at sundown if we need to.” 

“Please. Shhhhh” Fitz said testily. 

He laid down on his back and wriggled his way carefully under the floating cube that he’d been staring at for hours. He pulled a small battery powered soldering iron from his pocket and began poking around. A few minutes later, the cube opened like a flower. Fitz wriggled his way back out, practically throwing his tool in excitement. With the cube open, he could get a clearer view of the glowing orbs and mess of tubes. He threw his arms in the air.

“Ah ha! I’ve got it! I just need to...May, I shouldn’t need more than 20 minutes. Mack, pass the...no, not that, no, no, yes! That one!”

“Good to hear, Fitz.”

With a clear game plan, Fitz worked quickly. 

“See the genius of what I’m doing here,” he said happily to the team at large “is to make it look as though nothing was done at all! They will get here, look at the...the... the thingy, and think that while it is certainly alien, it is most certainly not a weapon. They’ll have- Mack, that over there, no, no, yes!- no reason to suspect anything. Weapon disarmed, Simmons cover maintained. Not bad if I say so myself.”

“Shit.”

“No, not shit, Agent May. Genius, pure-”

“Quiet Fitz. Skye, we’ve got company. It looks like 4 ops and...one scientist.”

“Copy that May. What’s the play?”

“Scientist? Do you mean Simmons? Is she here?”

“Shut up Fitz!” Skye and May said at the same time.

“Hide and ride it out.”

“Um, I don’t know if you’ve ever been in a pyramid May, but not a lot of spaces to hide...” Skye trailed off, scouting out the chamber.

“Well, figure it out. They’re entering the passage now. Pretty quickly too. Coulson, we need back up”

“On our way May. Fitz, is everything disabled?”

“I need 15 minutes.”

“You’ve got 10. Then you hide. No one is to engage. I repeat, do not engage. Do I make myself clear?” Coulson barked into his com.


	5. Chapter 5

**Notes for the Chapter:**

> I had hoped to finish this before the new episode made it obsolete, but no such luck. Last chapter should be up later this week. I hope you'll still read it even though it will diverge with the show.

“Nervous Simmons?”

Indeed, Jemma was nervous. She had done the math and the odds that Fitz had been here, disabled the weapon and left were not great. If she were a betting girl, she’d guess they were still here. 

“Hmm?”

“You’re shaking like a leaf.”

“Oh- yes. Well, I’m not so fond of confined spaces since my deep sea mishap. If you could ask Bakshi to keep that in mind for future missions, I’d be deeply appreciative.”

The Hydra agent, King, gave a noncommittal grunt. She’d never seen any of these agents before, but they seemed to be well schooled on her.

“Schneider, out in front. Simmons, you follow and I’ll be right behind you. You two, guard the entrance.”

They moved at pace faster than Jemma thought was wise, given the circumstances, and she made sure to voice these thoughts, loudly. If Fitz was here, she was going to give him plenty of warning.

“I am carrying very expensive, and considerably heavy equipment, through a poorly lit tunnel. Most people, with any common sense, would go slowly and carefully.”

They quickly came to the fork in the road, and when Schneider started down the descending passageway, Jemma squeaked loudly. All of Fitz’s sketches put the heart of the weapon in the subterranean chamber. If he were here, that is most certainly where he would be.

“Excuse me, um Schneider was it? Could we start with the upper chambers? I’m not really ready to head quite so deep underground just yet.”

King urged her forward on the descending path with the barrel of his gun. “We have to search the whole pyramid, might as well get the hardest part over with first.”

“Yes but-”

“Just walk Simmons and keep your voice down.” With his gun pushing into her shoulder blades, there was little she could say.


	6. Chapter 6

**Notes for the Chapter:**

> I had almost finished this a long time ago, but lost interest when it became AU. (because I am the worst.) At any rate, it started to bug me that I hadn't finished. So with apologies for tardiness and subpar editing, here is the last chapter.

Fitz began to shake at the sound of her voice. If anyone had noticed, he would have blamed it on his anger. He was furious with Jemma- furious with her for abandoning him, for risking her life like this after he sacrificed so much to keep her safe. But that wasn’t the whole truth, because he was also scared, and sad and happy. He felt everything all at once and the power of it made him weak in the knees.

He and Mack packed up the last of the tools as quietly as possible and hurried to the unfinished passageway carved in the south end of the chamber. A small dark dead end, it was the only place they could conceivably hide.

May came softly into their ears “Two agents stationed at the entrance. Stay put until everyone leaves.”

From the darkness, Fitz watched Jemma struggle with a large case. She silently unpacked the equipment while the two oafs she came in with uselessly stood guard. He couldn’t help the smug feeling of pride when he realized how superior their design was to the Hydra equipment she was using- the DWARFs would have made quick work of surveying the core. But as it was, Jemma was manually taking readings with a battery of clunky equipment. At this pace, they would be here all day.

Her guards seemed to be equally impatient. “Simmons, can you pick it up?”

She scanned the area, trying to judge how long this would take, when she spotted it- a small battery powered soldering pencil, clearly belonging to SHIELD. She quickly looked away, hoping that no one noticed.

But Fitz noticed. This was it, he was sure of it. Her cover was blown and they were all dead. And even if the soldering pencil didn’t give them away, surely the raucous thumping of his heart against his ribcage would.

Jemma was quick though. Without losing a second, she turned on one of the agents.

“When Bakshi asks why I didn’t properly measure the gamma radiation or identify the source isotopes, shall I go ahead and tell him that you and Schneider were in a bit of a hurry? Wanted to catch the football match?”

“Just shut up and work faster,” the agent mumbled.

“As I thought,” Jemma said in her told you so voice, with which Fitz was all to familiar. “Look, if you want to speed things up, perhaps you can scout out the upper chambers? Take this device. If there is anything even remotely resembling alien tech it will turn green. If it stays red the whole time, we can go as soon as I finish up here.”

Once the guards set off, Jemma released a big sigh and walked over to the offending item. She pocketed it and set back to work. She worked quickly, now that other agents were gone. Fitz was pleased to see a small smile flit across her face as she looked at the core and appreciated his work. She took a few more readings, wrote some things down and then packed up the equipment.

When she was finished, she stood awkwardly near the core, wringing her hands. It was a surefire sign that Jemma was struggling with some internal moral dilemma. Fitz smiled at the thought that no matter how much she had changed, he could still read her.

Without any warning, she bolted towards the small dark dead end that hid himself, Skye and Mack. As soon as she was completely in the shadow, she bent down and gently placed an object on the floor. Then just as quickly, she was back by the core.

When the guards came back just a few minutes later, she was seated on the large case, tapping her foot.

“Find anything worth examining, or should we try to catch the end of the match?” she teased lightly.

“Enough out of you,” the agent said, almost fondly. “Lets get back to HQ with that data.”

 

***

“Pack up and clear out,” May came in loud on the com once Hydra had left. The noise jarred Fitz, after sitting silently in the dark for so long.

Without a word, Skye walked over and picked up the object Simmons had left for them- the soldering pencil, wrapped in a single sheet of paper. She looked at it for a moment before handing it to Fitz.

Hands shaking, he unrolled the paper. In a hurried script Jemma had written-

_I miss you. Please don’t hate me._

Fitz handed the pencil to Mack and carefully pocketed the note.

That night, in the privacy of his bunk, Fitz reread the note over and over. Before stashing the note in an old but beloved textbook, he pulled out a pen and carefully wrote his reply-

_I could never hate you._


End file.
